from .allometry import add_allometry
from .basic_models import create_basic_pk_model
from .blq import transform_blq
from .common import (
    bump_model_number,
    convert_model,
    create_config_template,
    filter_dataset,
    get_config_path,
    get_model_code,
    get_model_covariates,
    load_example_model,
    print_model_code,
    print_model_symbols,
    read_model,
    read_model_from_string,
    remove_unused_parameters_and_rvs,
    rename_symbols,
    set_name,
    write_model,
)
from .compartments import get_bioavailability, get_lag_times
from .covariate_effect import (
    add_covariate_effect,
    get_covariates,
    has_covariate_effect,
    remove_covariate_effect,
)
from .data import (
    add_admid,
    add_cmt,
    add_time_after_dose,
    bin_observations,
    check_dataset,
    deidentify_data,
    drop_columns,
    drop_dropped_columns,
    expand_additional_doses,
    get_admid,
    get_baselines,
    get_cmt,
    get_concentration_parameters_from_data,
    get_covariate_baselines,
    get_doseid,
    get_doses,
    get_evid,
    get_ids,
    get_mdv,
    get_number_of_individuals,
    get_number_of_observations,
    get_number_of_observations_per_individual,
    get_observations,
    list_time_varying_covariates,
    load_dataset,
    read_dataset_from_datainfo,
    remove_loq_data,
    set_covariates,
    set_dvid,
    set_lloq_data,
    set_reference_values,
    translate_nmtran_time,
    undrop_columns,
    unload_dataset,
)
from .error import (
    has_additive_error_model,
    has_combined_error_model,
    has_proportional_error_model,
    has_weighted_error_model,
    remove_error_model,
    set_additive_error_model,
    set_combined_error_model,
    set_dtbs_error_model,
    set_iiv_on_ruv,
    set_power_on_ruv,
    set_proportional_error_model,
    set_time_varying_error_model,
    set_weighted_error_model,
    use_thetas_for_error_stdev,
)
from .estimation import calculate_parameters_from_ucp, calculate_ucp_scale
from .estimation_steps import (
    add_estimation_step,
    add_parameter_uncertainty_step,
    append_estimation_step_options,
    remove_estimation_step,
    remove_parameter_uncertainty_step,
    set_estimation_step,
    set_evaluation_step,
    set_simulation,
)
from .evaluation import (
    evaluate_epsilon_gradient,
    evaluate_eta_gradient,
    evaluate_expression,
    evaluate_individual_prediction,
    evaluate_population_prediction,
    evaluate_weighted_residuals,
)
from .expressions import (
    calculate_epsilon_gradient_expression,
    calculate_eta_gradient_expression,
    cleanup_model,
    create_symbol,
    get_dv_symbol,
    get_individual_parameters,
    get_individual_prediction_expression,
    get_observation_expression,
    get_parameter_rv,
    get_pd_parameters,
    get_pk_parameters,
    get_population_prediction_expression,
    get_rv_parameters,
    greekify_model,
    has_random_effect,
    is_linearized,
    is_real,
    make_declarative,
    mu_reference_model,
    simplify_expression,
)
from .iterators import omit_data, resample_data
from .math import (
    calculate_corr_from_cov,
    calculate_corr_from_prec,
    calculate_cov_from_corrse,
    calculate_cov_from_prec,
    calculate_prec_from_corrse,
    calculate_prec_from_cov,
    calculate_se_from_cov,
    calculate_se_from_prec,
)
from .metabolite import add_metabolite, has_presystemic_metabolite
from .odes import (
    add_bioavailability,
    add_individual_parameter,
    add_lag_time,
    add_peripheral_compartment,
    display_odes,
    find_clearance_parameters,
    find_volume_parameters,
    get_central_volume_and_clearance,
    get_initial_conditions,
    get_number_of_peripheral_compartments,
    get_number_of_transit_compartments,
    get_zero_order_inputs,
    has_first_order_absorption,
    has_first_order_elimination,
    has_instantaneous_absorption,
    has_linear_odes,
    has_linear_odes_with_real_eigenvalues,
    has_michaelis_menten_elimination,
    has_mixed_mm_fo_elimination,
    has_odes,
    has_seq_zo_fo_absorption,
    has_zero_order_absorption,
    has_zero_order_elimination,
    remove_bioavailability,
    remove_lag_time,
    remove_peripheral_compartment,
    set_first_order_absorption,
    set_first_order_elimination,
    set_initial_condition,
    set_instantaneous_absorption,
    set_michaelis_menten_elimination,
    set_mixed_mm_fo_elimination,
    set_ode_solver,
    set_peripheral_compartments,
    set_seq_zo_fo_absorption,
    set_transit_compartments,
    set_zero_order_absorption,
    set_zero_order_elimination,
    set_zero_order_input,
    solve_ode_system,
)
from .parameter_sampling import (
    create_rng,
    sample_individual_estimates,
    sample_parameters_from_covariance_matrix,
    sample_parameters_uniformly,
)
from .parameter_variability import (
    add_iiv,
    add_iov,
    add_pd_iiv,
    add_pk_iiv,
    create_joint_distribution,
    remove_iiv,
    remove_iov,
    split_joint_distribution,
    transform_etas_boxcox,
    transform_etas_john_draper,
    transform_etas_tdist,
    update_initial_individual_estimates,
)
from .parameters import (
    add_population_parameter,
    fix_or_unfix_parameters,
    fix_parameters,
    fix_parameters_to,
    get_omegas,
    get_sigmas,
    get_thetas,
    set_initial_estimates,
    set_lower_bounds,
    set_upper_bounds,
    unconstrain_parameters,
    unfix_parameters,
    unfix_parameters_to,
    update_inits,
)
from .pd import add_effect_compartment, add_indirect_effect, set_baseline_effect, set_direct_effect
from .plots import (
    plot_abs_cwres_vs_ipred,
    plot_cwres_vs_idv,
    plot_dv_vs_ipred,
    plot_dv_vs_pred,
    plot_individual_predictions,
    plot_iofv_vs_iofv,
    plot_transformed_eta_distributions,
)
from .random_variables import replace_non_random_rvs
from .results import (
    calculate_aic,
    calculate_bic,
    calculate_eta_shrinkage,
    calculate_individual_parameter_statistics,
    calculate_individual_shrinkage,
    calculate_pk_parameters_statistics,
    check_high_correlations,
    check_parameters_near_bounds,
)
from .tmdd import set_tmdd
from .units import get_unit_of
from .write_csv import write_csv

# Must be set directly, otherwise errors about unused imports
__all__ = [
    'add_admid',
    'add_cmt',
    'add_allometry',
    'add_parameter_uncertainty_step',
    'add_covariate_effect',
    'add_estimation_step',
    'add_effect_compartment',
    'add_indirect_effect',
    'add_iiv',
    'add_individual_parameter',
    'add_iov',
    'add_lag_time',
    'add_bioavailability',
    'add_metabolite',
    'add_peripheral_compartment',
    'add_pk_iiv',
    'add_pd_iiv',
    'add_population_parameter',
    'add_time_after_dose',
    'append_estimation_step_options',
    'bin_observations',
    'bump_model_number',
    'calculate_aic',
    'calculate_bic',
    'calculate_corr_from_cov',
    'calculate_corr_from_prec',
    'calculate_cov_from_corrse',
    'calculate_cov_from_prec',
    'calculate_epsilon_gradient_expression',
    'calculate_eta_gradient_expression',
    'calculate_eta_shrinkage',
    'calculate_individual_parameter_statistics',
    'calculate_individual_shrinkage',
    'calculate_prec_from_corrse',
    'calculate_prec_from_cov',
    'calculate_parameters_from_ucp',
    'calculate_pk_parameters_statistics',
    'calculate_se_from_cov',
    'calculate_se_from_prec',
    'calculate_ucp_scale',
    'check_dataset',
    'check_high_correlations',
    'check_parameters_near_bounds',
    'cleanup_model',
    'convert_model',
    'create_basic_pk_model',
    'create_config_template',
    'create_joint_distribution',
    'create_rng',
    'create_symbol',
    'deidentify_data',
    'display_odes',
    'drop_columns',
    'drop_dropped_columns',
    'evaluate_epsilon_gradient',
    'evaluate_eta_gradient',
    'evaluate_expression',
    'evaluate_individual_prediction',
    'evaluate_population_prediction',
    'evaluate_weighted_residuals',
    'expand_additional_doses',
    'filter_dataset',
    'find_clearance_parameters',
    'find_volume_parameters',
    'fix_or_unfix_parameters',
    'fix_parameters',
    'fix_parameters_to',
    'get_admid',
    'get_baselines',
    'get_bioavailability',
    'get_central_volume_and_clearance',
    'get_cmt',
    'get_concentration_parameters_from_data',
    'get_config_path',
    'get_covariates',
    'get_covariate_baselines',
    'get_doses',
    'get_doseid',
    'get_dv_symbol',
    'get_evid',
    'get_ids',
    'get_individual_parameters',
    'get_individual_prediction_expression',
    'get_initial_conditions',
    'get_lag_times',
    'get_mdv',
    'get_model_code',
    'get_model_covariates',
    'get_number_of_individuals',
    'get_number_of_observations',
    'get_number_of_observations_per_individual',
    'get_omegas',
    'get_observations',
    'get_observation_expression',
    'get_pk_parameters',
    'get_pd_parameters',
    'get_population_prediction_expression',
    'get_rv_parameters',
    'get_parameter_rv',
    'get_sigmas',
    'get_thetas',
    'get_unit_of',
    'get_zero_order_inputs',
    'greekify_model',
    'has_additive_error_model',
    'has_combined_error_model',
    'has_covariate_effect',
    'has_first_order_elimination',
    'has_linear_odes',
    'has_linear_odes_with_real_eigenvalues',
    'has_michaelis_menten_elimination',
    'has_mixed_mm_fo_elimination',
    'has_odes',
    'has_presystemic_metabolite',
    'has_proportional_error_model',
    'has_random_effect',
    'has_zero_order_absorption',
    'has_first_order_absorption',
    'has_instantaneous_absorption',
    'has_seq_zo_fo_absorption',
    'get_number_of_peripheral_compartments',
    'get_number_of_transit_compartments',
    'has_zero_order_elimination',
    'has_weighted_error_model',
    'is_linearized',
    'is_real',
    'list_time_varying_covariates',
    'load_dataset',
    'load_example_model',
    'make_declarative',
    'mu_reference_model',
    'omit_data',
    'plot_abs_cwres_vs_ipred',
    'plot_cwres_vs_idv',
    'plot_dv_vs_ipred',
    'plot_dv_vs_pred',
    'plot_individual_predictions',
    'plot_iofv_vs_iofv',
    'plot_transformed_eta_distributions',
    'print_model_code',
    'print_model_symbols',
    'read_dataset_from_datainfo',
    'read_model',
    'read_model_from_string',
    'rename_symbols',
    'remove_parameter_uncertainty_step',
    'remove_covariate_effect',
    'remove_error_model',
    'remove_estimation_step',
    'remove_iiv',
    'remove_iov',
    'remove_bioavailability',
    'remove_lag_time',
    'remove_loq_data',
    'remove_peripheral_compartment',
    'remove_unused_parameters_and_rvs',
    'replace_non_random_rvs',
    'resample_data',
    'sample_parameters_from_covariance_matrix',
    'sample_individual_estimates',
    'sample_parameters_uniformly',
    'set_additive_error_model',
    'set_baseline_effect',
    'set_instantaneous_absorption',
    'set_combined_error_model',
    'set_covariates',
    'set_direct_effect',
    'set_dtbs_error_model',
    'set_dvid',
    'set_estimation_step',
    'set_evaluation_step',
    'set_simulation',
    'set_first_order_absorption',
    'set_first_order_elimination',
    'set_iiv_on_ruv',
    'set_initial_condition',
    'set_initial_estimates',
    'set_lloq_data',
    'set_lower_bounds',
    'set_upper_bounds',
    'set_michaelis_menten_elimination',
    'set_mixed_mm_fo_elimination',
    'set_name',
    'set_ode_solver',
    'set_peripheral_compartments',
    'set_power_on_ruv',
    'set_proportional_error_model',
    'set_reference_values',
    'set_seq_zo_fo_absorption',
    'set_time_varying_error_model',
    'set_tmdd',
    'set_transit_compartments',
    'set_weighted_error_model',
    'set_zero_order_absorption',
    'set_zero_order_elimination',
    'set_zero_order_input',
    'simplify_expression',
    'solve_ode_system',
    'split_joint_distribution',
    'transform_blq',
    'transform_etas_boxcox',
    'transform_etas_john_draper',
    'transform_etas_tdist',
    'translate_nmtran_time',
    'unfix_parameters',
    'unfix_parameters_to',
    'update_initial_individual_estimates',
    'update_inits',
    'use_thetas_for_error_stdev',
    'write_csv',
    'write_model',
    'unconstrain_parameters',
    'undrop_columns',
    'unload_dataset',
]
